Genetic Diversity and Genomic Evolution of Microviridae Phages in the Human Respiratory Microbiome

Recent studies have revealed that Microviridae, a family of ssDNA viruses, are widely distributed in natural environments and play significant roles in various ecosystems. While Microviridae members dominate the human gut microbiome, their functions genetic diversity in the human respiratory ecosystem remain unclear. The distribution, genetic characteristics, and ecological roles of Microviridae are still poorly understood. This study identified 327 Microviridae-associated contigs from nasopharyngeal swab samples of healthy individuals through metagenomic sequencing and comparative genomics analysis, including 15 near-complete Microviridae-related genomes. These genomes exhibited high sequence divergence from each other, revealing their highly genetic diversity. Phylogenetic analysis based on VP1 (major capsid protein; F protein) demonstrated that the 15 genomes could be classified into seven distinct Microviridae groups. This work significantly expands the understanding of the diversity, genomic architecture, and evolutionary dynamics of Microviridae within the human respiratory tract.